From f5c31b33198288405f209773cd41a5efa1991e50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=B9=B2=E5=8A=B2?= Date: Tue, 1 Nov 2022 13:31:25 +0800 Subject: [PATCH 1/7] Add miss init --- .../models/science/unifold/modules/__init__.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 modelscope/models/science/unifold/modules/__init__.py diff --git a/modelscope/models/science/unifold/modules/__init__.py b/modelscope/models/science/unifold/modules/__init__.py new file mode 100644 index 00000000..9821d212 --- /dev/null +++ b/modelscope/models/science/unifold/modules/__init__.py @@ -0,0 +1,14 @@ +# Copyright 2021 DeepMind Technologies Limited +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""Data pipeline for model features.""" From 943478de635393e957bb0bf6ad677fdd189ac5c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=B9=B2=E5=8A=B2?= Date: Tue, 1 Nov 2022 13:32:57 +0800 Subject: [PATCH 2/7] Update --- .../models/science/unifold/modules/__init__.py | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/modelscope/models/science/unifold/modules/__init__.py b/modelscope/models/science/unifold/modules/__init__.py index 9821d212..63aa84ed 100644 --- a/modelscope/models/science/unifold/modules/__init__.py +++ b/modelscope/models/science/unifold/modules/__init__.py @@ -1,14 +1,3 @@ -# Copyright 2021 DeepMind Technologies Limited -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -"""Data pipeline for model features.""" +# The Uni-fold implementation is also open-sourced by the authors under Apache-2.0 license, +# and is publicly available at https://github.com/dptech-corp/Uni-Fold. +"""Unifold Modules.""" From 2759d538bb30c8c82d0dd32ea3b4bcd7606d41d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=B9=B2=E5=8A=B2?= Date: Tue, 1 Nov 2022 14:59:45 +0800 Subject: [PATCH 3/7] fix ut level for unifold --- tests/pipelines/test_unifold.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/pipelines/test_unifold.py b/tests/pipelines/test_unifold.py index df35dc5e..47bb7874 100644 --- a/tests/pipelines/test_unifold.py +++ b/tests/pipelines/test_unifold.py @@ -19,7 +19,7 @@ class UnifoldProteinStructureTest(unittest.TestCase, DemoCompatibilityCheck): self.protein_multimer = 'GAMGLPEEPSSPQESTLKALSLYEAHLSSYIMYLQTFLVKTKQKVNNKNYPEFTLFDTSKLKKDQTLKSIKT' + \ 'NIAALKNHIDKIKPIAMQIYKKYSKNIP' - @unittest.skipUnless(test_level() >= 2, 'skip test in current test level') + @unittest.skipUnless(test_level() >= 0, 'skip test in current test level') def test_run_by_direct_model_download(self): model_dir = snapshot_download(self.model_id) mono_pipeline_ins = pipeline(task=self.task, model=model_dir) From 30c8c27145261a3e5c7606976e11faef733d3f49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=B9=B2=E5=8A=B2?= Date: Tue, 1 Nov 2022 17:06:30 +0800 Subject: [PATCH 4/7] up requirements --- requirements/science.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/requirements/science.txt b/requirements/science.txt index 72994f72..c345da99 100644 --- a/requirements/science.txt +++ b/requirements/science.txt @@ -4,3 +4,5 @@ ml_collections scipy tensorboardX tokenizers +biopython +ipdb From 853e5235d56bf35922cde0db843cb62353e19a39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=B9=B2=E5=8A=B2?= Date: Tue, 1 Nov 2022 17:32:04 +0800 Subject: [PATCH 5/7] fix requirements --- requirements/science.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements/science.txt b/requirements/science.txt index c345da99..636f98f4 100644 --- a/requirements/science.txt +++ b/requirements/science.txt @@ -1,8 +1,8 @@ -iopath +biopython lmdb ml_collections scipy tensorboardX tokenizers -biopython -ipdb +iopath +ipdb \ No newline at end of file From 420b63f03b55d5c2a591fd69cd060ed3a8141ef4 Mon Sep 17 00:00:00 2001 From: "mulin.lyh" Date: Tue, 1 Nov 2022 17:44:18 +0800 Subject: [PATCH 6/7] fix style issues --- requirements/science.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements/science.txt b/requirements/science.txt index 636f98f4..c30ff644 100644 --- a/requirements/science.txt +++ b/requirements/science.txt @@ -1,8 +1,8 @@ biopython +iopath +ipdb lmdb ml_collections scipy tensorboardX tokenizers -iopath -ipdb \ No newline at end of file From aecb88044eba1789a675f22a32cc6f2eed71b91a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=B9=B2=E5=8A=B2?= Date: Tue, 1 Nov 2022 17:44:37 +0800 Subject: [PATCH 7/7] up --- requirements/science.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements/science.txt b/requirements/science.txt index 636f98f4..c30ff644 100644 --- a/requirements/science.txt +++ b/requirements/science.txt @@ -1,8 +1,8 @@ biopython +iopath +ipdb lmdb ml_collections scipy tensorboardX tokenizers -iopath -ipdb \ No newline at end of file